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New insights into the role of lipids in plant hypoxia responses

PROGRESS IN LIPID RESEARCH 2021年 81卷 101072-101072页

作者： Xie, Li-Juan Zhou, Ying Chen, Qin-Fang Xiao, Shi Sun Yat Sen Univ Sch Life Sci State Key Lab Biocontrol Guangdong Prov Key Lab Plant Resources Guangzhou 510275 Peoples R China Guangdong Lab Lingnan Modem Agr Guangzhou Peoples R China

In plants, hypoxia (low-oxygen stress) is induced by soil waterlogging or submergence and this major abiotic stress has detrimental effects on plant growth, development, distribution, and productivity. To survive low-oxygen stress, plants have evolved a set of morphological, physiological, and biochemical adaptations. These adaptations integrate metabolic acclimation and signaling networks allowing plants to endure or escape from low-oxygen environments by altering their metabolism and growth. Lipids are ubiquitously involved in regulating plant responses to hypoxia and post-hypoxic reoxygenation. In particular, the polyunsaturation of long-chain acyl-CoAs regulates hypoxia sensing in plants by modulating acyl-CoA-binding protein-Group VII ethylene response factor dynamics. Moreover, unsaturated very-long-chain ceramide species protect plants from hypoxia-induced cellular damage by regulating the kinase activity of CONSTITUTIVE TRIPLE RESPONSE1 in the ethylene signaling pathway. Finally, the oxylipin jasmonate specifically regulates plant responses to reoxygenation stress by transcriptionally modulating antioxidant biosynthesis. Here we provide an overview of the roles of lipid remodeling and signaling in plant responses to hypoxia/reoxygenation and their effects on the downstream events affecting plant survival. In addition, we highlight the key remaining challenges in this important field.

关键词： ABA abscisic acid ACBP acyl-CoA-binding protein AOC1 ALLENE OXIDE CYCLASE1 ATEs arginyl tRNA transferases ATP adenosine triphosphate bHLH basic helix-loop-helix CTR1 CONSTITUTIVE TRIPLE RESPONSE1 DGDG digalactosyldiacylglycerol EIN ETHYLENE INSENSITIVE ERF-VII group VII ethylene response factor FAD3 FATTY ACID DESATURASE3 GA gibberellin HIF1s hypoxia inducible factor 1 s JA jasmonic acid JAR1 JASMONATE RESISTANT1 LACS LONG-CHAIN ACYL-COA SYNTHETASE LCBs long-chain bases LOX1 LIPOXYGENASE1 LTP lipid transfer protein MetAP methionine aminopeptidase MGDG monogalactosyldiacylglycerol NO nitric oxide OPCL1 OPC-8:0-COA LIGASE1 OPR3 12-OXOPHYTODIENOATE REDUCTASE3 PA phosphatidic acid PC phosphatidylcholine PCOs plant cysteine oxidases PE phosphatidylethanolamine PG phosphatidylglycerol PHD prolyl hydroxylase domain PI phosphatidylinositol PRT6 PROTEOLYSIS6 PS phosphatidylserine ROS reactive oxygen species SAD6 stearoyl-acyl carrier protein Δ 9 -desaturase 6 VHL von Hippel-Lindau VLCFA very-long-chain fatty acid

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Maize bHLH55 functions positively in salt tolerance through modulation of AsA biosynthesis by directly regulating GDP-mannose pathway genes

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PLANT SCIENCE 2021年 302卷 110676-110676页

作者： Yu, Chunmei Yan, Ming Dong, Huizhen Luo, Jie Ke, Yongchao Guo, Anfang Chen, Yanhong Zhang, Jian Huang, Xiaosan Nantong Univ Sch Life Sci Minist Agr Sci Observing & Expt Stn Maize Plain Area Souther Nantong 226019 Peoples R China Nanjing Agr Univ Coll Hort 1 Weigang Nanjing 210095 Peoples R China

Ascorbic acid (AsA) is an antioxidant and enzyme co-factor that is vital to plant development and abiotic stress tolerance. However, the regulation mechanisms of AsA biosynthesis in plants remain poorly understood. Here, we report a basic helix-loop-helix 55 (ZmbHLH55) transcription factor that regulates AsA biosynthesis in maize. Analysis of publicly available transcriptomic data revealed that ZmbHLH55 is co-expressed with several genes of the GDP-mannose pathway. Experimental data showed that ZmbHLH55 forms homodimers localized to the cell nuclei, and it exhibits DNA binding and transactivation activity in yeast. Under salt stress conditions, knock down mutant (zmbhlh55) in maize accumulated lower levels of AsA compared with wild type, accompanied by lower antioxidant enzymes activity, shorter root length, and higher malondialdehyde (MDA) level. Gene expression data from the WT and zmbhlh55 mutant, showed that ZmbHLH55 positively regulates the expression of ZmPGI2, ZmGME1, and ZmGLDH, but negatively regulates ZmGMP1 and ZmGGP. Furthermore, ZmbHLH55-overexpressing Arabidopsis, under salt conditions, showed higher AsA levels, increased rates of germination, and elevated antioxidant enzyme activities. In conclusion, these results have identified previously unknown regulation mechanisms for AsA biosynthesis, indicating that ZmbHLH55 may be a potential candidate to enhance plant salt stress tolerance in the future.Y

关键词： Ascorbic acid basic helix-loop-helix GDP-mannose pathway Maize Salt stress tolerance

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Initial assessment of Id protein antagonist (aHLH) shows anti-proliferative activity on HEK293T, LS174T and HCT116 cells

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SCIENTIFIC AFRICAN 2022年 15卷

作者： Kyei, Foster Univ Cape Coast Sch Biol Sci Dept Mol Biol & Biotechnol Cape Coast Ghana

Id proteins (1-4) which are dominant-negative antagonists of the basic helix-loop-helix (bHLH) family of transcription factors function in a variety of cellular processes. They bind to the ubiquitously expressed 'E box' protein of the class A bHLH proteins (E12, E47, E2-2, and HEB). Each Id protein has distinct preferences and specificities for their E protein targets. A mutant version of E47 protein, an Id protein antagonist known as aHLH which is defective in DNA binding functions is known to suppress growth in hu-man carcinoma cell lines. This work investigates the effects of the Id protein antago-nist aHLH on growth and on pro-apoptotic functions in vitro using immortalized (highly tumorigenic) transformed human embryonic kidney cells (HEK293T), human epithelial colon adenocarcinoma cell line (LS174T) and human epithelial colon carcinoma cell line (HCT116). Plasmid encoding the aHLH proteins was transiently over-expressed in cultured HEK293T, LS174T and HCT116. Cell viability assay with MTT (3-(4, 5-Dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) was performed. Apoptotic and cell cycle assays were also performed on the transfected cells thereafter. Here, the results demonstrate that Id inhibition by aHLH impairs cell viability, inhibits cell proliferation and induces apoptosis in HEK293T, LS174T and HCT116 cell lines. These findings on the role of aHLH in cell growth and survival could help manipulate their functions as targets for developing anti-cancer agents and could also serve as molecular markers of human cancers.(c) 2022 The Author(s). Published by Elsevier B.V. on behalf of African Institute of Mathematical Sciences / Next Einstein Initiative. This is an open access article under the CC BY license ( http://***/licenses/by/4.0/ )

关键词： Id proteins aHLH basic helix-loop-helix Transcription factors Proliferation Apoptosis

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High-Throughput Affinity Measurements of Transcription Factor and DNA Mutations Reveal Affinity and Specificity Determinants

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CELL SYSTEMS 2021年第2期12卷 112-+页

作者： Aditham, Arjun K. Markin, Craig J. Mokhtari, Daniel A. DelRosso, Nicole Fordyce, Polly M. Stanford Univ Dept Bioengn Stanford CA 94305 USA Stanford Univ Stanford ChEM H Stanford CA 94305 USA Stanford Univ Dept Biochem Stanford CA 94305 USA Stanford Univ Grad Program Biophys Stanford CA 94305 USA Stanford Univ Dept Genet Stanford CA 94305 USA Chan Zuckerberg Biohub San Francisco CA 94110 USA

Transcription factors (TFs) bind regulatory DNA to control gene expression, and mutations to either TFs or DNA can alter binding affinities to rewire regulatory networks and drive phenotypic variation. While studies have profiled energetic effects of DNA mutations extensively, we lack similar information for TF variants. Here, we present STAMMP (simultaneous transcription factor affinity measurements via microfluidic protein arrays), a high-throughput microfluidic platform enabling quantitative characterization of hundreds of TF variants simultaneously. Measured affinities for similar to 210 mutants of a model yeast TF (Pho4) interacting with 9 oligonucleotides (>1,800 K(d)s) reveal that many combinations of mutations to poorly conserved TF residues and nucleotides flanking the core binding site alter but preserve physiological binding, providing a mechanism by which combinations of mutations in cis and trans could modulate TF binding to tune occupancies during evolution. Moreover, biochemical double-mutant cycles across the TF-DNA interface reveal molecular mechanisms driving recognition, linking sequence to function. A record of this paper's Transparent Peer Review process is included in the Supplemental Information.

关键词： transcriptional regulation microfluidics binding affinity protein-DNA binding transcription factor DNA specificity scanning mutagenesis conformational selection double-mutant cycle basic helix-loop-helix bHLH

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ZmbHLH80 and ZmbHLH90 transcription factors act antagonistically and contribute to regulate PEPC1 cell-specific gene expression in maize

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PLANT JOURNAL 2019年第2期99卷 270-285页

作者： Gorska, Alicja M. Gouveia, Paulo Borba, Ana R. Zimmermannw, Anna Serra, Tania S. Lourenco, Tiago F. Oliveira, Maria Margarida Peterhansel, Christoph Saibo, Nelson J. M. Univ Nova Lisboa Inst Tecnol Quim & Biol Antonio Xavier P-2780157 Oeiras Portugal Inst Biol Expt & Tecnol P-2780157 Oeiras Portugal Leibniz Univ Hannover Inst Bot Herrenhauser Str 3 D-30419 Hannover Germany

Compartmentation of photosynthetic reactions between mesophyll and bundle sheath cells is a key feature of C-4 photosynthesis and depends on the cell-specific accumulation of major C-4 enzymes, such as phosphoenolpyruvate carboxylase 1. The ZmPEPC1 upstream region, which drives light-inducible and mesophyll-specific gene expression in maize, has been shown to keep the same properties when introduced into rice (C-3 plant), indicating that rice has the transcription factors (TFs) needed to confer C-4-like gene expression. Using a yeast one-hybrid approach, we identified OsbHLH112, a rice basic helix-loop-helix (bHLH) TF that interacts with the maize ZmPEPC1 upstream region. Moreover, we found that maize OsbHLH112 homologues, ZmbHLH80, and ZmbHLH90, also interact with the ZmPEPC1 upstream region, suggesting that these C-4 regulators were co-opted from C-3 plants. A transactivation assay in maize mesophyll protoplasts revealed that ZmbHLH80 represses, whereas ZmbHLH90 activates, ZmPEPC1 expression. In addition, ZmbHLH80 was shown to impair the ZmPEPC1 promoter activation caused by ZmbHLH90. We showed that ZmbHLH80 and ZmbHLH90 bind to the same cis-element within the ZmPEPC1 upstream region either as homodimers or heterodimers. The formation of homo- and heterodimers with higher oligomeric forms promoted by ZmbHLH80 may explain its negative effect on gene transcription. Gene expression analysis revealed that ZmbHLH80 is preferentially expressed in bundle sheath cells, whereas ZmbHLH90 does not show a clear cell-specific expression pattern. Altogether, our results led us to propose a model in which ZmbHLH80 contributes to mesophyll-specific ZmPEPC1 gene expression by impairing ZmbHLH90-mediated ZmPEPC1 activation in the bundle sheath cells. Significance Statement Cell-specific accumulation of major C4 enzymes is a hallmark of C4 photosynthesis. The ZmPEPC1 upstream region is sufficient to drive mesophyll-specific gene expression in maize (C4 plant) and rice (C3 plant). He

关键词： C-4 photosynthesis phosphoenolpyruvate carboxylase basic helix-loop-helix Zea mays Oryza sativa mesophyll bundle sheath transcriptional regulation

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Transcriptional integration of the responses to iron availability in Arabidopsis by the bHLH factor ILR3

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NEW PHYTOLOGIST 2019年第3期223卷 1433-1446页

作者： Tissot, Nicolas Robe, Kevin Gao, Fei Grant-Grant, Susana Boucherez, Jossia Bellegarde, Fanny Maghiaoui, Amel Marcelin, Romain Izquierdo, Esther Benhamed, Moussa Martin, Antoine Vignols, Florence Roschzttardtz, Hannetz Gaymard, Frederic Briat, Jean-Francois Dubos, Christian Univ Montpellier BPMP CNRS INRASupAgro F-34060 Montpellier France Univ Paris Diderot Univ Paris Sud Inst Plant Sci Paris Saclay IPS2 UMR 9213UMR1403CNRSINRAUniv EvrySorbonne Par F-91405 Orsay France Pontificia Univ Catolica Chile Dept Genet Mol & Microbiol Santiago 8331150 Chile

Iron (Fe) homeostasis is crucial for all living organisms. In mammals, an integrated posttranscriptional mechanism couples the regulation of both Fe deficiency and Fe excess responses. Whether in plants an integrated control mechanism involving common players regulates responses both to deficiency and to excess is still to be determined. In this study, molecular, genetic and biochemical approaches were used to investigate transcriptional responses to both Fe deficiency and excess. A transcriptional activator of responses to Fe shortage in Arabidopsis, called bHLH105/ILR3, was found to also negatively regulate the expression of ferritin genes, which are markers of the plant's response to Fe excess. Further investigations revealed that ILR3 repressed the expression of several structural genes that function in the control of Fe homeostasis. ILR3 interacts directly with the promoter of its target genes, and repressive activity was conferred by its dimerisation with bHLH47/PYE. Last, this study highlighted that important facets of plant growth in response to Fe deficiency or excess rely on ILR3 activity. Altogether, the data presented herein support that ILR3 is at the centre of the transcriptional regulatory network that controls Fe homeostasis in Arabidopsis, in which it acts as both transcriptional activator and repressor.

关键词： Arabidopsis thaliana basic helix-loop-helix bHLH105 ferritins homeostasis ILR3 iron PYE

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Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells

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NEURAL DEVELOPMENT 2020年第1期15卷 5-5页

作者： Patoori, Sruti Jean-Charles, Nathalie Gopal, Ariana Sulaiman, Sacha Gopal, Sneha Wang, Brian Souferi, Benjamin Emerson, Mark M. CUNY Grad Ctr Biol PhD Program New York NY 10016 USA CUNY City Coll Dept Biol 138Th St & Convent Ave New York NY 10031 USA Rensselaer Polytech Inst Doctoral Program Dept Chem & Biol Engn Ctr Biotechnol & Interdisciplinary Studies Troy NY 12180 USA Touro Coll Ostepath Med New York NY 10027 USA CUNY Grad Ctr Biochem PhD Program New York NY 10016 USA

Background The vertebrate retina consists of six major classes of neuronal cells. During development, these cells are generated from a pool of multipotent retinal progenitor cells (RPCs) that express the gene Vsx2. Fate-restricted RPCs have recently been identified, with limited mitotic potential and cell fate possibilities compared to multipotent RPCs. One population of fate-restricted RPCs, marked by activity of the regulatory element ThrbCRM1, gives rise to both cone photoreceptors and horizontal cells. These cells do not express Vsx2, but co-express the transcription factors (TFs) Onecut1 and Otx2, which bind to ThrbCRM1. The components of the gene regulatory networks that control the transition from multipotent to fate-restricted gene expression are not known. This work aims to identify and evaluate cis-regulatory elements proximal to Onecut1 to identify the gene regulatory networks involved in RPC fate-restriction. Method We identified regulatory elements through ATAC-seq and conservation, followed by reporter assays to screen for activity based on temporal and spatial criteria. The regulatory elements of interest were subject to deletion and mutation analysis to identify functional sequences and evaluated by quantitative flow cytometry assays. Finally, we combined the enhancer::reporter assays with candidate TF overexpression to evaluate the relationship between the TFs, the enhancers, and early vertebrate retinal development. Statistical tests included ANOVA, Kruskal-Wallis, or unpaired t-tests. Results Two regulatory elements, ECR9 and ECR65, were identified to be active in ThrbCRM1(+) restricted RPCs. Candidate bHLH binding sites were identified as critical sequences in both elements. Overexpression of candidate bHLH TFs revealed specific enhancer-bHLH interactions. Nhlh1 overexpression expanded ECR65 activity into the Vsx2(+) RPC population, and overexpression of NeuroD1/NeuroG2/NeuroD4 had a similar effect on ECR9. Furthermore, bHLHs that were able to ac

关键词： Retinal progenitor cells Multipotent Fate-restricted Cone photoreceptors basic helix-loop-helix Chicken Electroporation

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A genome-wide identification and analysis of the basic helix-loop-helix transcription factors in the ponerine ant, Harpegnathos saltator

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BMC EVOLUTIONARY BIOLOGY 2012年第1期12卷 165-165页

作者： Liu, Ake Wang, Yong Dang, Chunwang Zhang, Debao Song, Huifang Yao, Qin Chen, Keping Jiangsu Univ Sch Food & Biol Engn Zhenjiang 212013 Peoples R China Jiangsu Univ Inst Life Sci Zhenjiang 212013 Peoples R China

Background: The basic helix-loop-helix (bHLH) transcription factors and their homologs form a superfamily that plays essential roles in transcriptional networks of multiple developmental processes. bHLH family members have been identified in over 20 organisms, including fruit fly, zebrafish, human and mouse. Result: In this study, we conducted a genome-wide survey for bHLH sequences, and identified 57 bHLH sequences encoded in complete genome sequence of the ponerine ant, Harpegnathos saltator. Phylogenetic analysis of the bHLH domain sequences classified these genes into 38 bHLH families with 23, 14, 10, 1, 8 and 1 members in group A, B, C, D, E and F, respectively. The number of PabHLHs (ponerine ant bHLHs) with introns is higher than many other insect species, and they are found to have introns with average lengths only inferior to those of pea aphid. In addition, two H. saltator bHLHs named PaCrp1 and PaSide locate on two separate contigs in the genome. Conclusions: A putative full set of PabHLH genes is comparable with other insect species and genes encoding Oligo, MyoRb and Figa were not found in genomes of all insect species of which bHLH family members have been identified. Moreover, in-family phylogenetic analyses indicate that the PabHLH genes are more closely related with Apis mellifera than others. The present study will serve as a solid foundation for further investigations into the structure and function of bHLH proteins in the regulation of H. saltator development.

关键词： basic helix-loop-helix Transcription factor Harpegnathos saltator Phylogenetic analysis Orthologous family Blast search

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C8orf46 homolog encodes a novel protein Vexin that is required for neurogenesis in Xenopus laevis

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DEVELOPMENTAL BIOLOGY 2018年第1期437卷 27-40页

作者： Moore, Kathryn B. Logan, Mary A. Aldiri, Issam Roberts, Jacqueline M. Steele, Michael Vetter, Monica L. Univ Utah Dept Neurobiol & Anat Salt Lake City UT 84112 USA Oregon Hlth & Sci Univ Dept Neurol Jungers Ctr Neurosci Res Portland OR 97239 USA St Jude Childrens Res Hosp Dept Dev Neurobiol 332 N Lauderdale St Memphis TN 38105 USA

Neural basic helix-loop helix (bHLH) transcription factors promote progenitor cell differentiation by activation of downstream target genes that coordinate neuronal differentiation. Here we characterize a neural bHLH target gene in Xenopus laeuis, uexin (vxn;previously sbt1), that is homologous to human c8orf46 and is conserved across vertebrate species. C8orf46 has been implicated in cancer progression, but its function is unknown. Vxn is transiently expressed in differentiating progenitors in the developing central nervous system (CNS), and is required for neurogenesis in the neural plate and retina. Its function is conserved, since overexpression of either Xenopus or mouse vxn expands primary neurogenesis and promotes early retinal cell differentiation in cooperation with neural bHLH factors. Vxn protein is localized to the cell membrane and the nucleus, but functions in the nucleus to promote neural differentiation. Vxn inhibits cell proliferation, and works with the cyclin-dependent kinase inhibitor p27Xic1 (cdkn1b) to enhance neurogenesis and increase levels of the proneural protein Neurog2. We propose that vxn provides a key link between neural bHLH activity and execution of the neurogenic program.

关键词： Neurogenesis basic helix-loop-helix P27 Cdkn1b Retina Xenopus laevis

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Synergistic Binding of bHLH Transcription Factors to the Promoter of the Maize NADP-ME Gene Used in C₄ Photosynthesis Is Based on an Ancient Code Found in the Ancestral C₃ State

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MOLECULAR BIOLOGY AND EVOLUTION 2018年第7期35卷 1690-1705页

作者： Borba, Ana Rita Serra, Tania S. Gorska, Alicja Gouveia, Paulo Cordeiro, Andre M. Reyna-Llorens, Ivan Knerova, Jana Barros, Pedro M. Abreu, Isabel A. Oliveira, Maria Margarida Hibberd, Julian M. Saibo, Nelson J. M. Univ Nova Lisboa Inst Tecnol Quim & Biol Antonio Xavier Oeiras Portugal Inst Biol Expt & Tecnol Oeiras Portugal Univ Cambridge Dept Plant Sci Cambridge England

C-4 photosynthesis has evolved repeatedly from the ancestral C-3 state to generate a carbon concentrating mechanism that increases photosynthetic efficiency. This specialized form of photosynthesis is particularly common in the PACMAD Glade of grasses, and is used by many of the world's most productive crops. The C-4 cycle is accomplished through cell-typespecific accumulation of enzymes but cis-elements and transcription factors controlling C-4 photosynthesis remain largely unknown. Using the NADP-Matic Enzyme (NADP-ME) gene as a model we tested whether mechanisms impacting on transcription in C-4 plants evolved from ancestral components found in C-3 species. Two basic helix-loop-helix (bHLH) transcription factors, ZmbHLH128 and ZmbHLH129, were shown to bind the C-4 NADP-ME promoter from maize. These proteins form heterodimers and ZmbHLH129 impairs trans-activation by ZmbHLH128. Electrophoretic mobility shift assays indicate that a pair of cis-elements separated by a seven base pair spacer synergistically bind either ZmbHLH128 or ZmbHLH129. This pair of cis-elements is found in both C-3 and C-4 Panicoid grass species of the PACMAD Glade. Our analysis is consistent with this cis-element pair originating from a single motif present in the ancestral C-3 state. We conclude that C-4 photosynthesis has co-opted an ancient C-3 regulatory code built on G-box recognition by bHLH to regulate the NADP-ME gene. More broadly, our findings also contribute to the understanding of gene regulatory networks controlling C-4 photosynthesis.

关键词： basic helix-loop-helix cis-element evolution C3 and C4 photosynthesis NADP-Malic Enzyme PACMAD Panicoid grasses

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